<div dir="ltr"><div>How many processors are you attempting to run on?<br></div>Is it possible to try a newer version of ParaView? The oldest that I have on my system is 4.4.0.<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jul 12, 2017 at 3:33 PM, Jake Gerard <span dir="ltr"><<a href="mailto:jake.a.gerard@gmail.com" target="_blank">jake.a.gerard@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Andy,<br></div><div><br></div>I wasn't setting up the server or anything. I have just been connecting to one of my preset configurations. The velocity data shows up fine but for some reason when there is more than one processor working on the visualization Paraview can't read it. <br><br></div>Here is the error:<br>
<p style="margin:0px;text-indent:0px"><span style="color:rgb(0,0,0)"><span style="font-family:"Courier";font-size:9pt">ERROR: In /p/home/angel/PV/4.3.1/Build_<wbr>4.3.1_osmesa/paraview/src/<wbr>paraview/VTK/IO/Xdmf2/<wbr>vtkXdmfHeavyData.cxx, line 1128</span></span></p><span style="color:rgb(0,0,0)">
</span><p style="margin:0px;text-indent:0px"><span style="color:rgb(0,0,0)"><span style="font-family:"Courier";font-size:9pt">vtkXdmfReader (0x104ae20): Failed to read attribute data</span></span></p><p style="margin:0px;text-indent:0px"><span style="color:rgb(0,0,0)"><span style="font-family:"Courier";font-size:9pt"><br></span></span></p><p style="margin:0px;text-indent:0px"><span style="color:rgb(0,0,0)"><span style="font-family:"Courier";font-size:9pt"><font face="arial,helvetica,sans-serif">The setup has just been clicking the connect icon, the system, and choosing the number of nodes and processors per node. If it helps I'm on Paraview 4.3.1 64-bit. Sorry I am pretty new to all of this stuff. Slowly getting the hang of things.<span class="HOEnZb"><font color="#888888"><br></font></span></font></span></span></p><span class="HOEnZb"><font color="#888888"><p style="margin:0px;text-indent:0px"><span style="color:rgb(0,0,0)"><span style="font-family:"Courier";font-size:9pt"><font face="arial,helvetica,sans-serif"><br></font></span></span></p><p style="margin:0px;text-indent:0px"><span style="color:rgb(0,0,0)"><span style="font-family:"Courier";font-size:9pt"><font face="arial,helvetica,sans-serif">Jake</font><br></span></span></p></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jul 12, 2017 at 1:48 PM, Andy Smith <span dir="ltr"><<a href="mailto:agsmith424@gmail.com" target="_blank">agsmith424@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div>Jake,<br><br></div>If I start up the remote server in parallel using something like:<br></div><span style="font-family:monospace,monospace">mpiexec.hydra -n 8 pvserver -sp=11111</span><br><br></div>and then connect from my workstation I am able to read an XDMF file like the one you posted using ParaView 5.4.0. Can you post how you are starting your server and the exact error that you receive?<br><br></div>I've attached the <span style="font-family:monospace,monospace">.xmf</span> file and a Python script to generate dummy data in a <span style="font-family:monospace,monospace">.h5</span> file that corresponds to your data structure.<br><br></div><div>Note that I am using the xdmf2 reader for my testing. The xdmf3 reader fails to read the file (even locally in serial) with the following error:<br><br><span style="font-family:monospace,monospace">Type not one of accepted values: INTEGER in XdmfArrayType::New<br>terminate called after throwing an instance of 'XdmfError'<br> what(): Type not one of accepted values: INTEGER in XdmfArrayType::New<br>Aborted</span><span class="m_-9030367541213066016HOEnZb"><font color="#888888"><br><br></font></span></div><span class="m_-9030367541213066016HOEnZb"><font color="#888888"><div><br></div>-Andy<br></font></span></div><div class="m_-9030367541213066016HOEnZb"><div class="m_-9030367541213066016h5"><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jul 12, 2017 at 1:31 PM, Jake Gerard <span dir="ltr"><<a href="mailto:jake.a.gerard@gmail.com" target="_blank">jake.a.gerard@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Alessandro,<br><br></div>Paraview says that it failed to read the attribute data. I just mean that when I connect Paraview to the machine, the pressure data does not load if I select more than 1 node or process/node.<span class="m_-9030367541213066016m_-1771926433853483111HOEnZb"><font color="#888888"><br><br></font></span></div><span class="m_-9030367541213066016m_-1771926433853483111HOEnZb"><font color="#888888">Jake<br></font></span></div><div class="m_-9030367541213066016m_-1771926433853483111HOEnZb"><div class="m_-9030367541213066016m_-1771926433853483111h5"><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jul 12, 2017 at 11:00 AM, Alessandro De Maio <span dir="ltr"><<a href="mailto:demaio.a@gmail.com" target="_blank">demaio.a@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Jake,<div> when you talk about running in multi-processing are you talking about the solver that produces the data or about running Paraview in mpi-mode?</div><div>Which is the error you get?</div><div><br></div><div>Alessandro</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="m_-9030367541213066016m_-1771926433853483111m_-2334505661057269610h5">On Wed, Jul 12, 2017 at 5:28 PM, Jake Gerard <span dir="ltr"><<a href="mailto:jake.a.gerard@gmail.com" target="_blank">jake.a.gerard@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="m_-9030367541213066016m_-1771926433853483111m_-2334505661057269610h5"><div dir="ltr">Any help here would be greatly appreciated.<br></div><div class="m_-9030367541213066016m_-1771926433853483111m_-2334505661057269610m_-1848549481505463284HOEnZb"><div class="m_-9030367541213066016m_-1771926433853483111m_-2334505661057269610m_-1848549481505463284h5"><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jul 11, 2017 at 2:37 PM, Jake Gerard <span dir="ltr"><<a href="mailto:jake.a.gerard@gmail.com" target="_blank">jake.a.gerard@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Good Afternoon,<br><br></div>I have been moving to an HDF5/XDMF system for analyzing big data from a computational fluid model. I finally got all the basic components working on my local machine but have run into problems when trying to run on an HPC system. Here is the XDMF file:<br><br><?xml version="1.0" ?><br><!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []><br><Xdmf xmlns:xi="<a href="http://www.w3.org/2003/XInclude" target="_blank">http://www.w3.org/20<wbr>03/XInclude</a>" Version="2.1"><br> <Domain><br> <Grid Name="my_Grid" GridType="Uniform"><br> <Topology TopologyType="3DCoRectMesh" Dimensions="91 19 19"><br> </Topology><br> <Geometry GeometryType="Origin_DxDyDz"><br> <DataItem Dimensions="3" NumberType="Integer" Format="XML"><br> 0 0 0<br> </DataItem><br> <DataItem Dimensions="3" NumberType="Integer" Format="XML"><br> 1 1 1<br> </DataItem><br> </Geometry><br> <Attribute Name="pressure" AttributeType="Scalar" Center="Node"><br> <DataItem Dimensions="91 19 19" NumberType="Float" Format="HDF"><br> out.h5:/pres_group/presmag<br> </DataItem><br> </Attribute><br> <Attribute Name="velocity" AttributeType="Vector" Center="Node"><br> <DataItem ItemType="Function" Function="JOIN($0, $1, $2)" Dimensions="91 19 19 3"><br> <DataItem Dimensions="91 19 19" NumberType="Float" Format="HDF"><br> out.h5:/velo_group/x_velo<br> </DataItem><br> <DataItem Dimensions="91 19 19" NumberType="Float" Format="HDF"><br> out.h5:/velo_group/y_velo<br> </DataItem><br> <DataItem Dimensions="91 19 19" NumberType="Float" Format="HDF"><br> out.h5:/velo_group/z_velo<br> </DataItem><br> </DataItem><br> </Attribute><br> </Grid><br> </Domain><br></Xdmf><br><br></div>This has worked properly on my machine. However, when I was getting an error of failing to read the pressure data when I tried this on multiple processes. The vector data for velocity was fine, but the pressure data could not be read. I narrowed the problem down to something regarding the number of processes because the pressure data worked fine on the HPC machine if I only ran it on 1 process. Is there anything that sticks out that could be causing this problem? For instance, is there a different format for these files when they are run on multiple processes?<br><br></div>Respectfully,<br><br></div>Jacob Gerard<br></div>
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